rs7246742

Positions:

• chr19-40839490-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.228 in 151,930 control chromosomes in the GnomAD database, including 5,199 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (5199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34602 AN: 151812 Hom.: 5192 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.226

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.228 AC: 34631 AN: 151930 Hom.: 5199 Cov.: 32 AF XY: 0.224 AC XY: 16651 AN XY: 74284

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.223

Alfa AF: 0.193 Hom.: 455

Bravo AF: 0.243

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7246742; hg19: chr19-41345395;